Problems with molecular mechanics implementations on the example of 4-benzoyl-1-(4-methyl-imidazol-5-yl)-carbonylthiosemicarbazide

No abstract is available for this paper.

• Publication year

  2012

• Venue

  Journal of Molecular Modeling

• Publication date

  2012-03-01

• Fields of study

  Medicine, Chemistry

• Identifiers
  DOI 10.1007/s00894-011-1117-1PMID 21625902
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Is conformational sampling of drug‐like molecules a solved problem?

  2011cited by this paper
• Effect of cyclodextrins on the solubility and stability of candesartan cilexetil in solution and solid state.

  2011cited by this paper
• Isoxazolidinyl polycyclic aromatic hydrocarbons as DNA-intercalating antitumor agents.

  2011cited by this paper
• Biological and docking studies of topoisomerase IV inhibition by thiosemicarbazides

  2011cited by this paper
• Unusual antimalarial meroditerpenes from tropical red macroalgae.

  2010cited by this paper
• Synthesis and pharmacological evaluation of novel fused thiophene derivatives as 5-HT2A receptor antagonists: molecular modeling study.

  2010cited by this paper
• Theoretical approach in the study of the inclusion processes of sulconazole with β-cyclodextrin

  2010cited by this paper
• Cyclodextrins as carriers for kavalactones in aqueous media: spectroscopic characterization of (S)-7,8-dihydrokavain and beta-cyclodextrin inclusion complex.

  2010cited by this paper
• Experimental verification of force fields for molecular dynamics simulations using Gly-Pro-Gly-Gly.

  2010cited by this paper
• Structural Fluctuations in Enzyme-Catalyzed Reactions: Determinants of Reactivity in Fatty Acid Amide Hydrolase from Multivariate Statistical Analysis of Quantum Mechanics/Molecular Mechanics Paths.

  2010cited by this paper
• Synthesis, spectral, thermal and theoretical studies of Cu(II) complexes with 3-[4′-dimethylaminophenyl]-1-(2-pyridyl)prop-2-en-1-one (DMAPP)

  2009cited by this paper
• Role of the conserved water molecules in the binding of inhibitor to IMPDH-II (human): A study on the water mimic inhibitor design

  2009cited by this paper
• Macrodipoles of potassium and chloride ion channels as revealed by electronic structure calculations

  2009cited by this paper
• Identification of small molecule regulators of the nuclear receptor HNF4alpha based on naphthofuran scaffolds.

  2009cited by this paper
• 13-Methyl-substituted des-C,D analogs of (20S)-1alpha,25-dihydroxy-2-methylene-19-norvitamin D3 (2MD): synthesis and biological evaluation.

  2009cited by this paper
• Synthesis and structural characterization of dicopper(II) and dipalladium(II) complexes of 1,1,2,2-tetrakis(carboxamido-2-methylpyridyl)ethane

  2009cited by this paper
• Gaussian 09W, revision A. 02

  2009cited by this paper
• Molecular modeling and inhibition of phospholipase A2 by polyhydroxy phenolic compounds.

  2009cited by this paper
• Copper and nickel binding in multi-histidinic peptide fragments.

  2009cited by this paper
• 3D entropy and moments prediction of enzyme classes and experimental-theoretic study of peptide fingerprints in Leishmania parasites.

  2009cited by this paper
• Aminoglycoside antibiotics: A-site specific binding to 16S

  2009cited by this paper
• Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions.

  2009cited by this paper
• SAR and QSAR studies: modelling of new DAPY derivatives.

  2008cited by this paper
• The His-His sequence of the antimicrobial peptide demegen P-113 makes it very attractive ligand for Cu2+.

  2008cited by this paper
• Structure-activity relationship analysis of N-benzoylpyrazoles for elastase inhibitory activity: a simplified approach using atom pair descriptors.

  2008cited by this paper
• Synthesis and antimicrobial activity of new 1,2,4-triazole and 1,3,4-thiadiazole derivatives.

  2008cited by this paper
• Epitope mapping and neuroprotective properties of a human single chain FV antibody that binds an internal epitope of amyloid-beta 1-42.

  2008cited by this paper
• Density functionals with broad applicability in chemistry.

  2008cited by this paper
• Screening of herbal constituents for aromatase inhibitory activity.

  2008cited by this paper
• Sulfonamide-1,2,4-triazole derivatives as antifungal and antibacterial agents: synthesis, biological evaluation, lipophilicity, and conformational studies.

  2008cited by this paper
• Synthesis and antimicrobial activity of new 1,2,4-triazole and 1,3,4-thiadiazole derivatives

  2008cited by this paper
• Sc(III) porphyrins. The molecular structure of two Sc(III) porphyrins and a re-evaluation of the parameters for the molecular mechanics modelling of Sc(III) porphyrins

  2008cited by this paper
• Comparative studies of coordination properties of puromycin and puromycin aminonucleoside towards copper(II) ions.

  2008cited by this paper
• Synthesis and antioxidant properties of novel N-methyl-1,3,4-thiadiazol-2-amine and 4-methyl-2H-1,2,4-triazole-3(4H)-thione derivatives of benzimidazole class.

  2008cited by this paper
• Exploration of physicochemical properties and molecular modelling studies of 2-sulfonyl-phenyl-3-phenyl-indole analogs as cyclooxygenase-2 inhibitors.

  2008cited by this paper
• Pentalenolactone biosynthesis. Molecular cloning and assignment of biochemical function to PtlF, a short-chain dehydrogenase from Streptomyces avermitilis , and identification of a new biosynthetic intermediate

  2008cited by this paper
• Mannosylation of mutated MBP83-99 peptides diverts immune responses from Th1 to Th2.

  2008cited by this paper
• Modulating the activity of avian pancreatic lipases by an alkyl chain reacting with an accessible sulfhydryl group.

  2007cited by this paper
• Solvatochromism, DNA binding, antitumor activity and molecular modeling study of mixed-ligand copper(II) complexes containing the bulky ligand: bis[N-(p-tolyl)imino]acenaphthene.

  2007cited by this paper
• Evaluation of chromatographic descriptors for the prediction of gastro-intestinal absorption of drugs.

  2007cited by this paper
• The action of the bacterial toxin, microcin B17, on DNA gyrase.

  2007cited by this paper
• Physico-chemical analysis of G-quadruplex containing bunch-oligonucleotides.

  2007cited by this paper
• Synthesis, characterization and biological activity of complexes of 2-hydroxy-3,5-dimethylacetophenoneoxime (HDMAOX) with copper(II), cobalt(II), nickel(II) and palladium(II).

  2007cited by this paper
• Novel and versatile methodology for synthesis of cyclic imides and evaluation of their cytotoxic, DNA binding, apoptotic inducing activities and molecular modeling study.

  2007cited by this paper
• Determination of the minimal fusion peptide of bovine leukemia virus gp30.

  2007cited by this paper
• Molecular organization of surfactin-phospholipid monolayers: effect of phospholipid chain length and polar head.

  2007cited by this paper
• Hydration energy of the 1,4-bonds of chitosan and their breakdown by ultrasonic treatment

  2007cited by this paper
• Synthesis, characterization and interaction with DNA of mononuclear metal complexes with oxolinic acid

  2007cited by this paper
• Synthesis, Structure Elucidation, and Biological Evaluation of Some Fused and/or Pendant Thiophene, Pyrazole, Imidazole, Thiazole, Triazole, Triazine, and Coumarin Systems Based on Cyanoacetic 2-[(Benzoylamino)thioxomethyl] Hydrazide

  2007cited by this paper
• Computational studies of the cyclization of thiosemicarbazides

  2007cited by this paper
• Conformation of oleuropein, the major bioactive compound of Olea europea

  2007cited by this paper
• Center-to-propeller and propeller-to-propeller stereocontrol in a series of macrobicyclic tri-λ5-phosphazenes

  2007cited by this paper
• A facile synthesis and highly atom economic 1,3-dipolar cycloaddition of hexahydropyrido[3,4-c][1,5]benzothiazepines with nitrile oxide: stereoselective formation of hexahydro[1,2,4]oxadiazolo[5,4-d]pyrido[3,4-c][1,5]benzothiazepines

  2007cited by this paper
• Design of Density Functionals by Combining the Method of Constraint Satisfaction with Parametrization for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions.

  2006cited by this paper
• QSAR study of mosquito repellents using Codessa Pro.

  2006cited by this paper
• The importance of outlier detection and training set selection for reliable environmental QSAR predictions.

  2006cited by this paper
• Stability of the guanine-cytosine radical cation in DNA base pairs triplets

  2006cited by this paper
• Encapsulation of 3-hydroxyflavone and fisetin in β-cyclodextrins : Excited state proton transfer fluorescence and molecular mechanics studies

  2006cited by this paper
• Distachyasin: A new antioxidant metabolite from the leaves of Carex distachya.

  2006cited by this paper
• Design and development of liposomes incorporating a bioactive labdane-type diterpene. In vitro growth inhibiting and cytotoxic activity against human cancer cell lines.

  2006cited by this paper
• Hydrophilically enhanced 3-carboranyl thymidine analogues (3CTAs) for boron neutron capture therapy (BNCT) of cancer.

  2006cited by this paper
• New chiral NiII complexes of Schiff's bases of glycine and alanine for efficient asymmetric synthesis of α-amino acids

  2006cited by this paper
• Synthesis, conformational characteristics and anti-influenza virus A activity of some 2-adamantylsubstituted azacycles.

  2006cited by this paper
• Conformational analysis of the N-terminal sequence Met1–Val60 of the tyrosine hydroxylase

  2006cited by this paper
• Apical uptake and transepithelial transport of sphingosine monomers through intact human intestinal epithelial cells: physicochemical and molecular modeling studies.

  2005cited by this paper
• The effect of overhanging nucleotides on fluorescence properties of hybridising oligonucleotides labelled with Alexa-488 and FAM fluorophores.

  2005cited by this paper
• Antimalarial activity of thioacridone compounds related to the acronycine alkaloid.

  2005cited by this paper
• Study of potential HIV-1 inhibition. Glutaric dialdehyde adducts

  2005cited by this paper
• Cyclic peptide models of the Ca2+-binding loop of α-lactalbumin

  2005cited by this paper
• Interaction of the 106-126 prion peptide with lipid membranes and potential implication for neurotoxicity.

  2005cited by this paper
• Optimization of polyurethane membranes: Morphology and structure studies

  2005cited by this paper
• Lewis acid-promoted transformation of 2-alkoxypyridines into 2-aminopyridines and their antibacterial activity. Part 2: Remarkably facile C-N bond formation.

  2005cited by this paper
• New acyclic receptors containing pyridazine units. The influence of π-stacking on the selective transport of lipophilic phenethylamines

  2005cited by this paper
• Complexation of Ketoconazole by Native and Modified Cyclodextrins

  2005cited by this paper
• Prediction of gastro-intestinal absorption using multivariate adaptive regression splines.

  2005cited by this paper
• Binding affinity difference induced by the stereochemistry of the sulfoxide bridge of the cyclic peptide inhibitors of Grb2-SH2 domain: NMR studies for the structural origin.

  2005cited by this paper
• Cyclic peptide models of the Ca2+-binding loop of alpha-lactalbumin.

  2005cited by this paper
• Classification of drugs in absorption classes using the classification and regression trees (CART) methodology.

  2005cited by this paper
• Mononuclear metal complexes with piroxicam: synthesis, structure and biological activity.

  2005cited by this paper
• Electronic density functional theory : recent progress and new directions

  1998cited by this paper
• All-atom empirical potential for molecular modeling and dynamics studies of proteins.

  1998cited by this paper
• Ab initio study of ionic solutions by a polarizable continuum dielectric model

  1998cited by this paper
• Continuum solvation models: A new approach to the problem of solute’s charge distribution and cavity boundaries

  1997cited by this paper
• A new integral equation formalism for the polarizable continuum model: Theoretical background and applications to isotropic and anisotropic dielectrics

  1997cited by this paper
• Density-functional thermochemistry.

  1996cited by this paper
• A second generation force field for the simulation of proteins

  1995cited by this paper
• Density-functional thermochemistry. III. The role of exact exchange

  1993cited by this paper
• The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin.

  1988cited by this paper
• Self‐consistent molecular orbital methods 25. Supplementary functions for Gaussian basis sets

  1984cited by this paper
• Efficient diffuse function‐augmented basis sets for anion calculations. III. The 3‐21+G basis set for first‐row elements, Li–F

  1983cited by this paper
• Contracted Gaussian basis sets for molecular calculations. I. Second row atoms, Z=11–18

  1980cited by this paper
• Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme.

  1976cited by this paper
• Self‐Consistent Molecular‐Orbital Methods. IX. An Extended Gaussian‐Type Basis for Molecular‐Orbital Studies of Organic Molecules

  1971cited by this paper

• Synergistic Effects of Thiosemicarbazides with Clinical Drugs against S. aureus

  2020cites this paper
• Systematic Identification of Thiosemicarbazides for Inhibition of Toxoplasma gondii Growth In Vitro

  2019cites this paper
• The protective role of macrophage migration inhibitory factor in acute kidney injury after cardiac surgery

  2018cites this paper
• Synthesis and Antibacterial Activity of New Thiazolidine-2,4-dione-Based Chlorophenylthiosemicarbazone Hybrids

  2018cites this paper
• Synthesis and antibacterial activity of 1,4-dibenzoylthiosemicarbazide derivatives

  2017cites this paper
• Preliminary Pharmacological Screening of Some Thiosemicarbazide, s-triazole, and Thiadiazole Derivatives.

  2016cites this paper
• Biological evaluation and molecular modelling study of thiosemicarbazide derivatives as bacterial type IIA topoisomerases inhibitors

  2016cites this paper
• Structure–activity Relationship Studies of Microbiologically Active Thiosemicarbazides Derived from Hydroxybenzoic Acid Hydrazides

  2015cites this paper
• 1,4-Disubstituted Thiosemicarbazide Derivatives are Potent Inhibitors of Toxoplasma gondii Proliferation

  2014cites this paper
• Pharmacological and Structure-Activity Relationship Evaluation of 4-aryl-1-Diphenylacetyl(thio)semicarbazides

  2014cites this paper
• Macrophage migration inhibitory factor in myocardial ischaemia/reperfusion injury.

  2014cites this paper
• Role of MIF in myocardial ischaemia and infarction: insight from recent clinical and experimental findings.

  2014cites this paper
• Synthesis, X-ray crystal structure and theoretical study of 4-ethyl-5-(2-thienyl)-2,4-dihydro-3H-1,2,4-triazole-3-thione; structural comparison with its aromatic analogs

  2011cites this paper
• Synthesis and structure-activity relationship studies of 4-arylthiosemicarbazides as topoisomerase IV inhibitors with Gram-positive antibacterial activity. Search for molecular basis of antibacterial activity of thiosemicarbazides.

  2011cites this paper